Indeed - thanks.
This was actually asked by a user of the rcdk package who is dealing with
InChI's.
The Java code you linked to is handy - what license is it available under?
if feasible, I'd like to include it in the rcdk package
On Fri, Feb 17, 2017 at 5:38 PM, John Mayfield <john.wilkinson...@gmail.com>
wrote:
> In general you shouldn't use InChI for storing (i.e. reading structures)
> it's unfortunate they made it possible. It is an identifier != exchange
> format, see Talk form Steve
> <http://www.hellers.com/steve/pub-talks/toronto-7-14.pdf>, Slide 8.
>
> That being said you can strip the salts and push it back through InChI
> (which has a neutralization algorithm - notice the formula is for the
> neutral form in your example), cut of the charge layer and then read it
> back. A disadvantage is since the layers are dependant you have to also
> drop the stereo as well. In this case it's actually okay to splice out the
> charge but in general that's not true.
>
> Charged Component:
> InChI=1S/C16H25N5O15P2/c17-13-7-14(19-3-18-13)21(4-20-7)15-
> 11(26)9(24)6(33-15)2-32-37(28,29)36-38(30,31)35-16-12(27)10(
> 25)8(23)5(1-22)34-16/h3-6,8-12,15-16,22-27H,1-2H2,(H,28,
> 29)(H,30,31)(H2,17,18,19)/p-2/t5-,6-,8-,9-,10+,11-,12-,15-,16?/m1/s1
>
> Neutral Component:
> InChI=1S/C16H25N5O15P2/c17-13-7-14(19-3-18-13)21(4-20-7)15-
> 11(26)9(24)6(33-15)2-32-37(28,29)36-38(30,31)35-16-12(27)10(
> 25)8(23)5(1-22)34-16/h3-6,8-12,15-16,22-27H,1-2H2,(H,28,
> 29)(H,30,31)(H2,17,18,19)/
>
> You'd also be surprised how far a very simple approach gets you:
> Neutralize.java
> <https://github.com/johnmay/mdk/blob/develop-1.5/tool/search-tree/src/main/java/org/openscience/cdk/isomorphism/Neutralise.java>
>
> John
>
> On 17 February 2017 at 14:00, Egon Willighagen <egon.willigha...@gmail.com
> > wrote:
>
>>
>> John suggest this list of SMARTS recently:
>>
>> http://www.daylight.com/meetings/emug00/Sayle/pkapredict.html
>>
>> And Nina mentioned code in AMBIT for SMIRKS to do the job...
>>
>> Egon
>>
>>
>>
>>
>> On Fri, Feb 17, 2017 at 2:51 PM, Rajarshi Guha <rajarshi.g...@gmail.com>
>> wrote:
>>
>>> Hi, I have a situtation where I start from an InChI for a molecule in
>>> salt form, and after stripping the salt, I would like to obtain the neutral
>>> form.
>>>
>>> An example is starting from
>>>
>>> InChI=1S/C16H25N5O15P2.2Na/c17-13-7-14(19-3-18-13)21(4-20-7)
>>> 15-11(26)9(24)6(33-15)2-32-37(28,29)36-38(30,31)35-16-12(27)
>>> 10(25)8(23)5(1-22)34-16;;/h3-6,8-12,15-16,22-27H,1-2H2,(H,28
>>> ,29)(H,30,31)(H2,17,18,19);;/q;2*+1/p-2/t5-,6-,8-,9-,10+,11
>>> -,12-,15-,16?;;/m1../s1
>>>
>>> I can use ConnectivityChecker to get the largest component. But this has
>>> a charge of -2, with the phosphate groups missing a proton.
>>>
>>> Is there a convenience method to neutralize this molecule by adding
>>> protons appropriately?
>>>
>>> --
>>> Rajarshi Guha | http://blog.rguha.net
>>> NIH Center for Advancing Translational Science
>>>
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>>>
>>
>>
>> --
>> E.L. Willighagen
>> Department of Bioinformatics - BiGCaT
>> Maastricht University (http://www.bigcat.unimaas.nl/)
>> Homepage: http://egonw.github.com/
>> LinkedIn: http://se.linkedin.com/in/egonw
>> Blog: http://chem-bla-ics.blogspot.com/
>> PubList: http://www.citeulike.org/user/egonw/tag/papers
>> ORCID: 0000-0001-7542-0286
>> ImpactStory: https://impactstory.org/u/egonwillighagen
>>
>> ------------------------------------------------------------
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>>
>
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--
Rajarshi Guha | http://blog.rguha.net
NIH Center for Advancing Translational Science
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